ArticleNucleic acids research2012
Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
34 citing papers in PubMed, 62 citations in OpenAlex.
- Biology of host-dependent restriction-modification in prokaryotes.EcoSal Plus · 2025Review
- Bacterial restriction-modification systems: mechanisms of defense against phage infection.Biophysics reports · 2025Article
- Prophage-encoded methyltransferase drives adaptation of community-acquired methicillin-resistant Staphylococcus aureus.The Journal of clinical investigation · 2025Article
- Synthesizing supercoiled circular DNA molecules in vitro.Nucleic acids research · 2025Article
- D7A Mutagenesis and In Silico Analysis on Haloacid Dehalogenase Gene from Pseudomonas aeruginosa ITB1 in pET/ACS omega · 2025Article
- Structural analysis of the BisI family of modification dependent restriction endonucleases.Nucleic acids research · 2024Article
- Mutations found in cancer patients compromise DNA binding of the winged helix protein STK19.Scientific reports · 2024Article
- Review
- Circular PCR as an efficient and precise umbrella of methods for the generation of circular dsDNA with staggered nicks: Mechanism and types.Biology methods & protocols · 2024Article
- Characterization of winged helix domain fusion endonucleases as N6-methyladenine-dependent type IV restriction systems.Frontiers in microbiology · 2024Article
- Navigating the pitfalls of mapping DNA and RNA modifications.Nature reviews. Genetics · 2023Review
- In Silico Discovery of Anticancer Peptides from Sanghuang.International journal of molecular sciences · 2022Article
- Light Dependent Changes in Adenylate Methylation of the Promoter of the Mitochondrial Citrate Synthase Gene in Maize (International journal of molecular sciences · 2022Article
- Quick Access to Nucleobase-Modified Phosphoramidites for the Synthesis of Oligoribonucleotides Containing Post-Transcriptional Modifications and Epitranscriptomic Marks.The Journal of organic chemistry · 2022Article
- Genome Study of a Novel Virulent Phage vB_SspS_KASIA and Mu-like Prophages ofInternational journal of molecular sciences · 2021Article
- Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA.Nucleic acids research · 2021Article
- Identification, Characterization, and Genomic Analysis of NovelInternational journal of molecular sciences · 2020Article
- Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å.Nucleic acids research · 2020Article
- Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties.PLoS computational biology · 2020Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
Abstract
DNA methylation-dependent restriction enzymes have many applications in genetic engineering and in the analysis of the epigenetic state of eukaryotic genomes. Nevertheless, high-resolution structures have not yet been reported, and therefore mechanisms of DNA methylation-dependent cleavage are not understood. Here, we present a biochemical analysis and high-resolution DNA co-crystal structure of the N(6)-methyladenine (m6A)-dependent restriction enzyme R.DpnI. Our data show that R.DpnI consists of an N-terminal catalytic PD-(D/E)XK domain and a C-terminal winged helix (wH) domain. Surprisingly, both domains bind DNA in a sequence- and methylation-sensitive manner. The crystal contains R.DpnI with fully methylated target DNA bound to the wH domain, but distant from the catalytic domain. Independent readout of DNA sequence and methylation by the two domains might contribute to R.DpnI specificity or could help the monomeric enzyme to cut the second strand after introducing a nick.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.